Cells depend on contact with their outside environment in order to thrive. Two examples illustrate why: In one, information needed to guide cellular processes is constantly transmitted across cell membranes by specialized proteins, and in the other, maintaining the right gradient of ions across the membrane is a process critical to the life and death of a cell. Membrane transport proteins—functioning either as channels or transporters—are the gatekeepers that control contact with the world outside the cell by catalyzing the flow of ions and molecules across cell membranes. Malfunctioning transport proteins can lead to cancer, inflammatory, and neurological diseases. Despite their importance in cell function and in a multitude of physiological processes such as sensing pain, there are still many unknowns about how they function. Recently, in an impressive series of three papers in Nature and Science, researchers at the Oregon Health and Science University delineated the structures of three transporter proteins, one of which had never before been characterized structurally in such detail. The structures were solved using ALS Beamlines 5.0.2, 8.2.1, and 8.2.2.

Delivering the Goods to Cells

Each of the cells in our bodies is like a tiny city, bustling with the commerce of daily life. And like a city, which cannot thrive in isolation from the rest of the world, cell survival also depends on contact with its outside environment. In addition to taking in food and oxygen-bearing molecules and expelling waste products and secretions such as hormones through the membrane that surrounds it, a cell needs information from outside to help control processes within; it also needs to maintain the right balance of ions inside and outside the cell, a balance on which its life and death depends. Akin to the guardians at old-time city gates who controlled the flux of "goods" through the city walls, specialized membrane transport proteins catalyze the flow across cell membranes of the ions that maintain the balance and of the molecules that constitute the information.

Plainly, understanding how membrane transport proteins function in detail is a high priority for life sciences researchers. Yet, despite their importance as well as the severe consequences when the transporters malfunction (e.g., cancer, inflammatory, and neurological diseases), there are still many unknowns about how they function. Recently, researchers at the Oregon Health and Science University, using x-ray crystallography at the ALS, solved the atomic structures of three important transporter proteins, structures that provide some of the information needed to fill in the gaps.

Two of the protein structures solved were ion channels: the P2X receptor, which is ATP activated, and an acid-sensing ion channel (ASIC). The researchers had predicted that these two proteins would have different topologies, but were surprised to discover that the proteins showed remarkable similarity in their structures, despite large differences in their function and in their amino acid sequences. They are both trimers, each consisting of three protein strands that angle sharply through the membrane and wrap slightly around one another, creating a chalice-like structure. Both contain "vestibules" outside the membrane, where ions might be directed and might serve a regulatory role, as well as a central pore that opens and closes as necessary to allow ions to traverse the membrane.

The structure of the P2X receptor revealed grooves, located on sections of the protein outside the membrane, that most likely serve as ATP binding sites. These binding sites were unique, representing an entirely new ATP binding motif. The structure also suggested a way in which ATP binding leads to the large structural changes involved in opening the central pore: the ATP binding site is lined with a series of amino acids that face the groove, as well as several that face away, allowing information to be transmitted from the binding site to the rest of the structure. The ASIC structure, in contrast, is proton-activated and allows only sodium ions in or out of the cell. By soaking cesium ions into crystals of this protein and solving the x-ray structure with the cesium bound in several places, the scientists were able to pinpoint specific ion-binding sites within the vestibules and central pore, suggesting the path that ions might take through the pore.

Left: The P2X receptor is chalice-shaped, with three protein strands (colored red, blue, and yellow) angling steeply through the cell membrane. Right: A large portion of the protein sits outside the membrane and contains "vestibules" and a central pore, as shown in the cutaway surface figure. The electrostatic potential of the surface is colored red to blue, as indicated.

The third structure was an amino-acid transporter with a very different architecture. This type of transporter is involved in diverse physiological processes from blood-pressure regulation to digestion and neurotransmission. In contrast to the ion-channel structures, this protein is located almost entirely within the membrane, without the extracellular vestibules available for ion localization. Twelve helices span the membrane in a cylindrical structure that is organized to allow a solvent-accessible channel to penetrate deep within the transporter. The scientists used the structure to suggest a way in which proton binding to a specific amino acid changes the conformation of one of the helices and opens the channel, allowing a direct path from outside to inside the cell. This mechanism for transport is very similar to sodium-coupled transporters, showing how the structural mechanism for transport can be conserved among different types of proteins.

In contrast to the receptor proteins, the amino-acid transporter sits almost entirely within the cell membrane. Twelve alpha helices span the membrane and can shift in a way that opens a pore through the membrane.

Research funding: National Institutes of Health, New York Consortium for Membrane Protein Structure, National Asthma Foundation, and Howard Hughes Medical Institute. Operation of the ALS is supported by the U.S. Department of Energy, Office of Basic Energy Sciences.